Hx, a Novel Fluorescent, Minor Groove and Sequence Specific Recognition Element: Design, Synthesis, and DNA Binding Properties of p-Anisylbenzimidazole-imidazole/pyrrole-Containing Polyamides

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• 作者：Sameer Chavda ; Yang Liu ; Balaji Babu ; Ryan Davis ; Alan Sielaff ; Jennifer Ruprich ; Laura Westrate ; Christopher Tronrud ; Amanda Ferguson ; Andrew Franks ; Samuel Tzou ; Chandler Adkins ; Toni Rice ; Hilary Mackay ; Jerome Kluza ; Sharjeel A Tahir ; Shicai Lin ; Konstantinos Kiakos ; Chrystal D. Bruce ; W. David Wilson ; John A. Hartley ; Moses Lee
• 刊名：Biochemistry
• 出版年：2011
• 出版时间：April 19, 2011
• 年：2011
• 卷：50
• 期：15
• 页码：3127-3136
• 全文大小：1095K
• 年卷期：v.50,no.15(April 19, 2011)
• ISSN：1520-4995

文摘

With the aim of incorporating a recognition element that acts as a fluorescent probe upon binding to DNA, three novel pyrrole (P) and imidazole (I)-containing polyamides were synthesized. The compounds contain a p-anisylbenzimidazolecarboxamido (Hx) moiety attached to a PP, IP, or PI unit, giving compounds HxPP (2), HxIP (3), and HxPI (4), respectively. These fluorescent hybrids were tested against their complementary nonfluorescent, non-formamido tetraamide counterparts, namely, PPPP (5), PPIP (6), and PPPI (7) (cognate sequences 5鈥?AAATTT-3鈥? 5鈥?ATCGAT-3鈥? and 5鈥?ACATGT-3鈥? respectively). The binding affinities for both series of polyamides for their cognate and noncognate sequences were ascertained by surface plasmon resonance (SPR) studies, which revealed that the Hx-containing polyamides gave binding constants in the 10⁶ M^鈭? range while little binding was observed for the noncognates. The binding data were further compared to the corresponding and previously reported formamido-triamides f-PPP (8), f-PIP (9), and f-PPI (10). DNase I footprinting studies provided additional evidence that the Hx moiety behaved similarly to two consecutive pyrroles (PP found in 5鈭?b>7), which also behaved like a formamido-pyrrole (f-P) unit found in distamycin and many formamido-triamides, including 8鈭?b>10. The biophysical characterization of polyamides 2鈭?b>7 on their binding to the abovementioned DNA sequences was determined using thermal melts (螖T_M), circular dichroism (CD), and isothermal titration calorimetry (ITC) studies. Density functional calculations (B3LYP) provided a theoretical framework that explains the similarity between PP and Hx on the basis of molecular electrostatic surfaces and dipole moments. Furthermore, emission studies on polyamides 2 and 3 showed that upon excitation at 322 nm binding to their respective cognate sequences resulted in an increase in fluorescence at 370 nm. These low molecular weight polyamides show promise for use as probes for monitoring DNA recognition processes in cells.